EP1265582A2 - Polynucleotides et polypeptides associes au colon et au cancer du colon - Google Patents

Polynucleotides et polypeptides associes au colon et au cancer du colon

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Publication number
EP1265582A2
EP1265582A2 EP00966944A EP00966944A EP1265582A2 EP 1265582 A2 EP1265582 A2 EP 1265582A2 EP 00966944 A EP00966944 A EP 00966944A EP 00966944 A EP00966944 A EP 00966944A EP 1265582 A2 EP1265582 A2 EP 1265582A2
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EP
European Patent Office
Prior art keywords
seq
residues
include those
sequence shown
epitopes include
Prior art date
Legal status (The legal status is an assumption and is not a legal conclusion. Google has not performed a legal analysis and makes no representation as to the accuracy of the status listed.)
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Application number
EP00966944A
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German (de)
English (en)
Inventor
Steven M. Ruben
Steven C. Barash
Charles E. Birse
Craig A. Rosen
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Human Genome Sciences Inc
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Human Genome Sciences Inc
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Application filed by Human Genome Sciences Inc filed Critical Human Genome Sciences Inc
Publication of EP1265582A2 publication Critical patent/EP1265582A2/fr
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    • C—CHEMISTRY; METALLURGY
    • C07—ORGANIC CHEMISTRY
    • C07K—PEPTIDES
    • C07K14/00—Peptides having more than 20 amino acids; Gastrins; Somatostatins; Melanotropins; Derivatives thereof
    • C07K14/435—Peptides having more than 20 amino acids; Gastrins; Somatostatins; Melanotropins; Derivatives thereof from animals; from humans
    • C07K14/46—Peptides having more than 20 amino acids; Gastrins; Somatostatins; Melanotropins; Derivatives thereof from animals; from humans from vertebrates
    • C07K14/47—Peptides having more than 20 amino acids; Gastrins; Somatostatins; Melanotropins; Derivatives thereof from animals; from humans from vertebrates from mammals
    • A—HUMAN NECESSITIES
    • A61—MEDICAL OR VETERINARY SCIENCE; HYGIENE
    • A61P—SPECIFIC THERAPEUTIC ACTIVITY OF CHEMICAL COMPOUNDS OR MEDICINAL PREPARATIONS
    • A61P35/00—Antineoplastic agents
    • C—CHEMISTRY; METALLURGY
    • C12—BIOCHEMISTRY; BEER; SPIRITS; WINE; VINEGAR; MICROBIOLOGY; ENZYMOLOGY; MUTATION OR GENETIC ENGINEERING
    • C12Q—MEASURING OR TESTING PROCESSES INVOLVING ENZYMES, NUCLEIC ACIDS OR MICROORGANISMS; COMPOSITIONS OR TEST PAPERS THEREFOR; PROCESSES OF PREPARING SUCH COMPOSITIONS; CONDITION-RESPONSIVE CONTROL IN MICROBIOLOGICAL OR ENZYMOLOGICAL PROCESSES
    • C12Q1/00—Measuring or testing processes involving enzymes, nucleic acids or microorganisms; Compositions therefor; Processes of preparing such compositions
    • C12Q1/68—Measuring or testing processes involving enzymes, nucleic acids or microorganisms; Compositions therefor; Processes of preparing such compositions involving nucleic acids
    • C12Q1/6876—Nucleic acid products used in the analysis of nucleic acids, e.g. primers or probes
    • C12Q1/6883—Nucleic acid products used in the analysis of nucleic acids, e.g. primers or probes for diseases caused by alterations of genetic material
    • C12Q1/6886—Nucleic acid products used in the analysis of nucleic acids, e.g. primers or probes for diseases caused by alterations of genetic material for cancer
    • C—CHEMISTRY; METALLURGY
    • C12—BIOCHEMISTRY; BEER; SPIRITS; WINE; VINEGAR; MICROBIOLOGY; ENZYMOLOGY; MUTATION OR GENETIC ENGINEERING
    • C12Q—MEASURING OR TESTING PROCESSES INVOLVING ENZYMES, NUCLEIC ACIDS OR MICROORGANISMS; COMPOSITIONS OR TEST PAPERS THEREFOR; PROCESSES OF PREPARING SUCH COMPOSITIONS; CONDITION-RESPONSIVE CONTROL IN MICROBIOLOGICAL OR ENZYMOLOGICAL PROCESSES
    • C12Q2600/00—Oligonucleotides characterized by their use
    • C12Q2600/136—Screening for pharmacological compounds

Definitions

  • This invention relates to newly identified colon or colon cancer related polynucleotides and the polypeptides encoded by these polynucleotides herein collectively known as "colon cancer antigens," and the use of such colon cancer antigens for targeting specific cell types and/or diagnosing, detecting, preventing and treating disorders disorders of the colon, particularly the presence of colon cancer and colon cancer metastases.
  • This invention relates to colon cancer antigens as well as vectors, host cells, antibodies directed to colon cancer antigens and the recombinant or synthetic methods for producing the same. Also provided are diagnostic methods for diagnosing and treating, preventing and/or prognosing disorders related to the colon, including colon cancer, and therapeutic methods for treating such disorders.
  • the invention further relates to screening methods for identifying agonists and antagonists of colon cancer antigens of the invention.
  • the present invention further relates to inhibiting the production and function of the polypeptides of the present invention.
  • Colorectal cancers are among the most common cancers in men and women in the U.S. and are one of the leading causes of death. Other than surgical resection no other systemic or adjuvant therapy is available. Vogelstein and colleagues have described the sequence of genetic events that appear to be associated with the multistep process of colon cancer development in humans (Trends Genet 9(4):138-41 (1993)). An understanding of the molecular genetics of carcinogenesis, however, has not led to preventative or therapeutic measures. It can be expected that advances in molecular genetics will lead to better risk assessment and early diagnosis but colorectal cancers will remain a deadly disease for a majority of patients due to the lack of an adjuvant therapy.
  • Colorectal carcinoma is a malignant neoplastic disease.
  • Tumors of this type often metastasize through lymphatic and vascular channels.
  • Many patients with colorectal carcinoma eventually die from this disease.
  • the only systemic treatment available for colon cancer is chemotherapy.
  • MDR gene that codes for multi-drug resistance gene products.
  • the MDR gene products actively transport the toxic substances out of the cell before the chemotherapeutic agents can damage the DNA machinery of the cell. These toxic substances harm the normal cell populations more than they harm the colon cancer cells for the above reasons.
  • This invention relates to newly identified colon and colon cancer related polynucleotides and the polypeptides encoded by these polynucleotides herein collectively known as "colon cancer antigens.”
  • This invention relates to colon and colon cancer related polypeptides as well as vectors, host cells, antibodies directed to colon cancer antigens and the recombinant methods for producing the same. Also provided are diagnostic methods for diagnosing and treating, preventing and/or prognosing disorders related to the colon, including colon cancer, and therapeutic methods for treating such disorders.
  • the invention further relates to screening methods for identifying agonists and antagonists of colon cancer antigens ofthe invention.
  • Table 1 summarizes some of the colon cancer antigens encompassed by the invention
  • the first column shows the "SEQ ID NO:X" for each ofthe 4277 colon and colon cancer related polynucleotide sequences of the invention.
  • the second column provides a unique "Sequence/Contig ID” identification for each of the colon and colon cancer related polynucleotide and/or polypeptide sequences.
  • the third column, "Gene Name,” and the fourth column, “Overlap,” provide a putative identification of the gene based on the sequence similarity of its translation product to an amino acid sequence found in a publicly accessible gene database and the database accession no. for the database sequence having similarity, respectively.
  • the sixth and seventh columns provide the location (nucleotide position nos. within the sequence/contig), "Start” and “End”, in the polynucleotide sequence "SEQ ED NO:X” that delineate the preferred ORF shown in the sequence listing as SEQ ID NO:Y (column five).
  • the eighth and ninth columns provide the "%Id” (percent identity) and "%Si” (percent similarity), respectively, observed between the aligned sequence segments of the translation product of SEQ ED NO:X and the database sequence.
  • the tenth column provides a unique "Clone ID:Z” for a cDNA clone related to each contig sequence.
  • the eleventh column provides the "Cloning vector" contained in the cDNA clone ID.
  • Table 2 summarizes ATCC Deposits, Deposit dates, and ATCC designation numbers of deposits made with the ATCC in connection with the present application.
  • Table 3 summarizes the expression profile of polynucleotides corresponding to the clones disclosed in Table 1.
  • the first column provides a unique clone identifier, "Clone TD", for a cDNA clone related to each contig sequence disclosed in Table 1.
  • Column 2 "Library Codes" shows the expression profile of tissue and/or cell line libraries which express the polynucleotides of the invention.
  • Each Library Code in column 2 represents a tissue/cell source identifier code corresponding to the Library Code and Library description provided in Table 5. Expression of these polynucleotides was not observed in the other tissues and/or cell libraries tested.
  • One of skill in the art could routinely use this information to identify tissues which show a predominant expression pattern of the corresponding polynucleotide of the invention or to identify polynucleotides which show predominant and/or specific tissue expression.
  • Table 4 column 1, provides a nucleotide sequence identifier, "SEQ ID NO:X,” that matches a nucleotide SEQ ID NO:X disclosed in Table 1, column 5.
  • Table 4, column 2, provides the chromosomal location, "Cytologic Band or Chromosome,” of polynucleotides corresponding to SEQ ID NO:X. Chromosomal location was determined by finding exact matches to EST and cDNA sequences contained in the NCBI (National Center for Biotechnology Information) UniGene database. Given a presumptive chromosomal location, disease locus association was determined by comparison with the Morbid Map, derived from Online Mendelian Inheritance in Man (Online Mendelian Inheritance in Man, OMIMTM.
  • Table 6 provides a key to the OMIM reference identification numbers disclosed in Table 4, column 3.
  • OMIM reference identification numbers (Column 1) were derived from Online Mendelian Inheritance in Man (Online Mendelian Inheritance in Man, OMIM. McKusick-Nathans Institute for Genetic Medicine, Johns Hopkins University (Baltimore, MD) and National Center for Biotechnology Information, National Library of Medicine, (Bethesda, MD) 2000. World Wide Web URL: http://www.ncbi.nlm.nih.gov/omim/).
  • Column 2 provides diseases associated with the cytologic band disclosed in Table 4, column 2, as determined using the Morbid Map database.
  • Table 7 indicates public ESTs, of which at least one, two, three, four, five, ten, fifteen or more of any one or more of these public EST sequences are optionally excluded from certain embodiments of the invention.
  • Table 8 lists residues comprising antigenic epitopes of anti genie epitope-bearing fragments present in each of the preferred ORFs (SEQ ED NO:Y) encoded by the colon or colon cancer related polynucleotides described in Table 1 as predicted by the inventors using the algorithm of Jameson and Wolf, (1988) Comp. Appl. Biosci. 4:181-186.
  • Colon and/or colon cancer related polypeptides shown in Table 1 may possess one or more antigenic epitopes comprising residues described in Table 8. It will be appreciated that depending on the analytical criteria used to predict antigenic determinants, the exact address of the determinant may vary slightly.
  • the residues and locations shown described in Table 8 correspond to the amino acid sequences for each colon and/or colon cancer related polypeptide sequence shown in the Sequence Listing.
  • Table 9 shows the cDNA libraries sequenced, and ATCC designation numbers and vector information relating to these cDNA libraries.
  • isolated refers to material removed from its original environment (e.g., the natural environment if it is naturally occurring), and thus is altered “by the hand of man” from its natural state.
  • an isolated polynucleotide could be part of a vector or a composition of matter, or could be contained within a cell, and still be “isolated” because that vector, composition of matter, or particular cell is not the original environment of the polynucleotide.
  • isolated does not refer to genomic or cDNA libraries, whole cell total or mRNA preparations, genomic DNA preparations (including those separated by electrophoresis and transferred onto blots), sheared whole cell genomic DNA preparations or other compositions where the art demonstrates no distinguishing features of the polynucleotide/sequences of the present invention.
  • a "polynucleotide” refers to a molecule having a nucleic acid sequence contained in SEQ ID NO:X or the cDNA clone deposited with the ATCC.
  • the polynucleotide can contain the nucleotide sequence of the full length cDNA sequence, including the 5' and 3' untranslated sequences, the coding region, as well as fragments, epitopes, domains, and variants of the nucleic acid sequence.
  • a "polypeptide” refers to a molecule having the translated amino acid sequence generated from the polynucleotide as broadly defined.
  • SEQ ED NO:X was often generated by overlapping sequences contained in multiple clones (contig analysis).
  • a representative clone containing all or most of the sequence for SEQ ID NO:X is deposited at Human Genome Sciences, Inc. (HGS) in a catalogued and archived library.
  • HGS Human Genome Sciences, Inc.
  • Table 1 each clone is identified by a cDNA Clone ID (Identifier).
  • Each Clone ID is unique to an individual clone and the Clone ID is all the information needed to retrieve a given clone from the HGS library.
  • the cDNA clones were deposited at the American Type Culture Collection (hereinafter "ATCC").
  • Table 1 correlates the Clone ID names with SEQ ID NOs. Furthermore, it is possible to retrieve a given cDNA clone from the ATCC deposit by techniques known in the art and described elsewhere herein.
  • the ATCC is located at 10801 University Boulevard, Manassas, Virginia 20110-2209, USA.
  • the ATCC deposits were made persuant to the terms of the Budapest Treaty on the international recognition of the deposit of microorganisms for the p poses of patent procedure.
  • the polynucleotides of the invention are at least 15, at least 30, at least 50, at least 100, at least 125, at least 500, or at least 1000 continuous nucleotides but are less than or equal to 300 kb, 200 kb, 100 kb, 50 kb, 15 kb, 10 kb, 7.5kb, 5 kb, 2.5 kb, 2.0 kb, or 1 kb, in length.
  • polynucleotides of the invention comprise a portion of the coding sequences, as disclosed herein, but do not comprise all or a portion of any intron.
  • the polynucleotides comprising coding sequences do not contain coding sequences of a genomic flanking gene (i.e., 5' or 3' to the gene of interest in the genome). In other embodiments, the polynucleotides of the invention do not contain the coding sequence of more than 1000, 500, 250, 100, 50, 25, 20, 15, 10, 5, 4, 3, 2, or 1 genomic flanking gene(s).
  • a "polynucleotide” of the present invention also includes those polynucleotides capable of hybridizing, under stringent hybridization conditions, to sequences contained in SEQ ID NO:X, the complement thereof, or the cDNA clone within the pool of cDNA clones deposited with the ATCC.
  • “Stringent hybridization conditions” refers to an overnight incubation at 42 degree C in a solution comprising 50% formamide, 5x SSC (750 mM NaCl, 75 mM trisodium citrate), 50 mM sodium phosphate (pH 7.6), 5x Denhardt's solution, 10% dextran sulfate, and 20 ⁇ g/ml denatured, sheared salmon sperm DNA, followed by washing the filters in 0.1 x SSC at about 65 degree C.
  • nucleic acid molecules that hybridize to the polynucleotides of the present invention at lower stringency hybridization conditions. Changes in the stringency of hybridization and signal detection are primarily accomplished through the manipulation of formamide concentration (lower percentages of formamide result in lowered stringency); salt conditions, or temperature.
  • washes performed following stringent hybridization can be done at higher salt concentrations (e.g. 5X SSC).
  • blocking reagents include Denhardt's reagent, BLOTTO, heparin, denatured salmon sperm DNA, and commercially available proprietary formulations.
  • the inclusion of specific blocking reagents may require modification of the hybridization conditions described above, due to problems with compatibility.
  • polynucleotide which hybridizes only to polyA+ sequences (such as any 3' terminal polyA+ tract of a cDNA shown in the sequence listing), or to a complementary stretch of T (or U) residues, would not be included in the definition of "polynucleotide,” since such a polynucleotide would hybridize to any nucleic acid molecule containing a poly (A) stretch or the complement thereof (e.g., practically any double-stranded cDNA clone generated using oligo dT as a primer).
  • polynucleotide of the present invention can be composed of any polyribonucleotide or polydeoxribonucleotide, which may be unmodified RNA or DNA or modified RNA or DNA.
  • polynucleotides can be composed of single- and double-stranded DNA, DNA that is a mixture of single- and double-stranded regions, single- and double-stranded RNA, and RNA that is mixture of single- and double-stranded regions, hybrid molecules comprising DNA and RNA that may be single-stranded or, more typically, double-stranded or a mixture of single- and double-stranded regions.
  • polynucleotide can be composed of triple-stranded regions comprising RNA or DNA or both RNA and DNA.
  • a polynucleotide may also contain one or more modified bases or DNA or RNA backbones modified for stability or for other reasons.
  • Modified bases include, for example, tritylated bases and unusual bases such as inosine.
  • a variety of modifications can be made to DNA and RNA; thus, "polynucleotide” embraces chemically, enzymatically, or metabolically modified forms.
  • the polypeptide of the present invention can be composed of amino acids joined to each other by peptide bonds or modified peptide bonds, i.e., peptide isosteres, and may contain amino acids other than the 20 gene-encoded amino acids.
  • the polypeptides may be modified by either natural processes, such as posttranslational processing, or by chemical modification techniques which are well known in the art. Such modifications are well described in basic texts and in more detailed monographs, as well as in a voluminous research literature. Modifications can occur anywhere in a polypeptide, including the peptide backbone, the amino acid side-chains and the amino or carboxyl termini.
  • polypeptides may be branched , for example, as a result of ubiquitination, and they may be cyclic, with or without branching. Cyclic, branched, and branched cyclic polypeptides may result from posttranslation natural processes or may be made by synthetic methods.
  • Modifications include acetylation, acylation, ADP-ribosylation, amidation, covalent attachment of flavin, covalent attachment of a heme moiety, covalent attachment of a nucleotide or nucleotide derivative, covalent attachment of a lipid or lipid derivative, covalent attachment of phosphotidylinositol, cross-linking, cyclization, disulfide bond formation, demethyl ation, formation of covalent cross-links, formation of cysteine, formation of pyroglutamate, formylation, gamma-carboxylation, glycosylation, GPI anchor formation, hydroxylation, iodination, methylation, myristoylation, oxidation, pegylation, proteolytic processing, phosphorylation, prenylation, racemization, selenoylation, sulfation, transfer- RNA mediated addition of amino acids to proteins such as arginylation, and ubiquitination.
  • SEQ ID NO:X refers to a polynucleotide sequence while “SEQ ID NO:Y” refers to a polypeptide sequence.
  • SEQ ID NO:X is identified by an integer specified in column 1 of Table 1.
  • a translated open reading frame (ORF) encoded by polynucleotide SEQ ID NO:X, SEQ ID NO:Y, is shown in column nine of Table 1.
  • ORF open reading frame
  • 4277 colon and/or colon cancer related polypeptide sequences shown in the sequence listing one polypeptide sequence for each of the polynucleotide sequences.
  • the polynucleotide sequences are shown in the sequence listing immediately followed by all of the polypeptide sequences.
  • a polypeptide having biological activity refers to polypeptides exhibiting activity similar, but not necessarily identical to, an activity of a polypeptide of the present invention, including mature forms, as measured in a particular biological assay, with or without dose dependency. In the case where dose dependency does exist, it need not be identical to that of the polypeptide, but rather substantially similar to the dose-dependence in a given activity as compared to the polypeptide of the present invention (i.e., the candidate polypeptide will exhibit greater activity or not more than about 25-fold less and, preferably, not more than about tenfold less activity, and most preferably, not more than about three-fold less activity relative to the polypeptide of the present invention).
  • polynucleotides of the invention may be arrayed onto a nitrocellulose filter and screened with labelled mRNA which has been isolated from particular normal or diseased tissues, as described in Example 3.
  • Known polynucleotide sequences are included in the array as hybridization controls, either because of their demonstrated tissue specificity or because they represent known surface molecules which may after further study show a predominant tissue expression and be useful antibody targets.
  • polynucleotides described in Table 1 are expressed at significantly enhanced levels in human colon and colon cancer tissues. Accordingly, such polynucleotides, polypeptides encoded by such polynucleotides, and antibodies specific for such polypeptides find use in the prediction, diagnosis, treatment, and prevention of disorders related to the colon, including, but not limited to colon cancer, as more fully described below.
  • Table 1 summarizes some of the polynucleotides encompassed by the invention (including polynucleotide sequences (SEQ ID NO:X) and the related cDNA clones (Clone ID:Z)) and further summarizes certain characteristics of these colon and/or colon cancer related polynucleotides, and the polypeptides encoded thereby.
  • the first column of Table 1 shows the "SEQ ID NO:X" for each of the 4277 polynucleotide sequences of the invention.
  • the second column provides a unique "Sequence/Contig ED" for each sequence.
  • the third column in Table 1 "Gene Name" provides a putative identification of the gene based on the sequence similarity of its translation product to an a ino acid sequence found in a publicly accessible gene database, such as GenBank (NCBI). Methods for determining such sequence similarity are described in Example 1 , below. The great majority of the cDNA sequences reported in Table 1 are unrelated to any sequences previously described in the literature.
  • the fourth column in Table 1, "Overlap,” provides the database accession no. for the database sequence having similarity.
  • the preferred translated amino acid sequence is identified in column five as "AA SEQ ID NO:Y," although other reading frames can also be easily translated using known molecular biology techniques.
  • the polypeptides produced by these alternative open reading frames are specifically contemplated by the present invention.
  • Polynucleotides encoding an amino acid sequence comprising these regions are also embodied, as are polynucleotides which hybridize to polynucleotides encoding these regions.
  • the sixth and seventh columns in Table 1 provide the location (nucleotide position nos.), "Start” and “End,” in the polynucleotide sequence "SEQ ID NO:X” that aligns with homologous database sequence.
  • the invention provides a polypeptide comprising an amino acid sequence encoded by the portion of SEQ ED NO:X delineated by "Start” and "End”. Also provided are polynucleotides encoding such polypeptides.
  • the eighth and ninth columns provide the "%Id” (percent identity) and "% Si"
  • SEQ ID NO:X and the translated SEQ ID NO:Y are sufficiently accurate and otherwise suitable for a variety of uses well known in the art and described further below.
  • SEQ ID NO:X is useful for designing nucleic acid hybridization probes that will detect nucleic acid sequences contained in SEQ ID NO:X or the cDNA contained in the deposited clone. These probes will also hybridize to nucleic acid molecules in biological samples, thereby enabling immediate applications in chromosome mapping, linkage analysis, tissue identification and/or typing, and a variety of forensic and diagnostic methods of the invention.
  • polypeptides identified from SEQ ID NO:Y may be used to generate antibodies which bind specifically to the colon and/or colon cancer related antigen polypeptides encoded by the cDNA clones identified in Table 1.
  • DNA sequences generated by sequencing reactions can contain sequencing errors.
  • the errors exist as misidentified nucleotides, or as insertions or deletions of nucleotides in the generated DNA sequence.
  • the erroneously inserted or deleted nucleotides cause frame shifts in the reading frames of the predicted amino acid sequence.
  • the predicted amino acid sequence diverges from the actual amino acid sequence, even though the generated DNA sequence may be greater than 99.9% identical to the actual DNA sequence (for example, one base insertion or deletion in an open reading frame of over 1000 bases).
  • the present invention provides not only the generated nucleotide sequence identified as SEQ ID NO:X and the predicted translated amino acid sequence identified as SEQ ID NO:Y, but also a sample of plasmid DNA containing a human cDNA of the invention deposited with the ATCC, as set forth in Table 1.
  • the nucleotide sequence of each deposited clone can readily be determined by sequencing the deposited clone in accordance with known methods. The predicted amino acid sequence can then be verified from such deposits.
  • the amino acid sequence of the protein encoded by a particular clone can also be directly determined by peptide sequencing or by expressing the protein in a suitable host cell containing the deposited human cDNA, collecting the protein, and determining its sequence.
  • the present invention also relates to vectors or plasmids which include such DNA sequences, as well as the use of the DNA sequences.
  • Table 2 shows the material deposited with the ATCC, the Deposit Date and the ATCC Designation Number.
  • each is a mixture of cDNA clones derived from a variety of human tissue and cloned in either a plasmid vector or a phage vector, as shown in Table 9. These deposits are referred to as "the deposits” herein.
  • the tissues from which the clones were derived are listed in Table 9, and the vector in which the cDNA is contained is also indicated in Table 9 as well as Table 1.
  • the deposited material includes the cDNA clones which were partially sequenced and listed in Table 1. Thus, the DNA sequence of Table 1 is only a portion of the sequence included in the clone from which the sequence was derived.
  • a clone which is isolatable from the ATCC Deposits by use of a sequence listed in Table 1 may include the entire coding region of a human gene or in other cases such clone may include a substantial portion of the coding region of a human gene.
  • sequence listing lists only a portion of the DNA sequence in a clone included in the ATCC Deposits, it is well within the ability of one skilled in the art to complete the sequence of the DNA included in a clone isolatable from the ATCC Deposits by use of a sequence (or portion thereof) listed in Table 1 by procedures hereinafter further described, and others apparent to those skilled in the art.
  • the present invention also relates to the genes corresponding to SEQ ID NO:X, SEQ ID NO:Y, or the deposited clone.
  • the corresponding gene can be isolated in accordance with known methods using the sequence information disclosed herein. Such methods include preparing probes or primers from the disclosed sequence and identifying or amplifying the corresponding gene from appropriate sources of genomic material. Also provided in the present invention are allelic variants, orthologs, and/or species homologs.
  • Procedures known in the art can be used to obtain full-length genes, allelic variants, splice variants, full-length coding portions, orthologs, and/or species homologs of genes corresponding to SEQ ID NO:X, SEQ ID NO:Y, or the deposited clone, using information from the sequences disclosed herein or the libraries deposited with the ATCC.
  • allelic variants and/or species homologs may be isolated and identified by making suitable probes or primers from the sequences provided herein and screening a suitable nucleic acid source for allelic variants and/or the desired homologue.
  • Table 3 summarizes the expression profile of polynucleotides corresponding to the clones disclosed in Table 1.
  • the first column provides a unique clone identifier, "Clone ID:Z”, for a cDNA clone related to each contig sequence disclosed in Table 1.
  • Column 2 "Library Codes” shows the expression profile of tissue and/or cell line libraries which express the polynucleotides of the invention.
  • Each Library Code in column 2 represents a tissue/cell source identifier code corresponding to the Library Code and Library description provided in Table 5. Expression of these polynucleotides was not observed in the other tissues and/or cell libraries tested.
  • One of skill in the art could routinely use this information to identify tissues which show a predominant expression pattern of the corresponding polynucleotide of the invention or to identify polynucleotides which show predominant and/or specific tissue expression.
  • Table 4 column 1, provides a nucleotide sequence identifier, "SEQ ID NO:X,” that matches a nucleotide SEQ ID NO:X disclosed in Table 1, column 5.
  • Table 4, column 2, provides the chromosomal location, "Cytologic Band or Chromosome,” of polynucleotides corresponding to SEQ ID NO:X. Chromosomal location was determined by finding exact matches to EST and cDNA sequences contained in the NCBI (National Center for Biotechnology Information) UniGene database. Given a presumptive chromosomal location, disease locus association was determined by comparison with the Morbid Map, derived from Online Mendelian Inheritance in Man (Online Mendelian Inheritance in Man, OMIMTM.
  • Table 6 provides a key to the OMIM reference identification numbers disclosed in Table 4, column 3.
  • OMIM reference identification numbers (Column 1) were derived from Online Mendelian Inheritance in Man (Online Mendelian Inheritance in Man, OMIM. McKusick-Nathans Institute for Genetic Medicine, Johns Hopkins University (Baltimore, MD) and National Center for Biotechnology Information, National Library of Medicine, (Bethesda, MD) 2000. World Wide Web URL: http://www.ncbi.nlm.nih.gov/omim/).
  • Column 2 provides diseases associated with the cytologic band disclosed in Table 4, column 2, as determined using the Morbid Map database.
  • polypeptides of the invention can be prepared in any suitable manner.
  • Such polypeptides include isolated naturally occurring polypeptides, recombinantly produced polypeptides, synthetically produced polypeptides, or polypeptides produced by a combination of these methods. Means for preparing such polypeptides are well understood in the art.
  • polypeptides may be in the form of the secreted protein, including the mature form, or may be a part of a larger protein, such as a fusion protein (see below). It is often advantageous to include an additional amino acid sequence which contains secretory or leader sequences, pro-sequences, sequences which aid in purification, such as multiple histidine residues, or an additional sequence for stability during recombinant production.
  • polypeptides of the present invention are preferably provided in an isolated form, and preferably are substantially purified.
  • a recombinantly produced version of a polypeptide, including the secreted polypeptide can be substantially purified using techniques described herein or otherwise known in the art, such as, for example, by the one- step method described in Smith and Johnson, Gene 67:31-40 (1988).
  • Polypeptides of the invention also can be purified from natural, synthetic or recombinant sources using techniques described herein or otherwise known in the art, such as, for example, antibodies of the invention raised against the colon cancer antigens in methods which are well known in the art.
  • the present invention provides a polynucleotide comprising, or alternatively consisting of, the nucleic acid sequence of SEQ ID NO:X, and/or a cDNA contained in the ATCC deposit.
  • the present invention also provides a polypeptide comprising, or alternatively, consisting of, the polypeptide sequence of SEQ ID NO:Y and/or a polypeptide encoded by a cDNA contained in the ATCC deposit.
  • Polynucleotides encoding a polypeptide comprising, or alternatively consisting of the polypeptide sequence of SEQ ID NO:Y and/or a polypeptide sequence encoded by a cDNA contained in the ATCC deposits are also encompassed by the invention.
  • polynucleotide sequences such as EST sequences
  • sequence databases are publicly available and accessible through sequence databases and may have been publicly available prior to conception of the present invention.
  • related polynucleotides are specifically excluded from the scope of the present invention. To list every related sequence would unduly burden the disclosure of this application. Accordingly, for each "Contig Id" listed in the third column of Table 7, preferably excluded are one or more polynucleotides comprising a nucleotide sequence described in the second column of Table 7 by the general formula of a-b, each of which are uniquely defined for the SEQ ID NO:X corresponding to that Contig Id in the fourth column of Table 7.
  • specific embodiments are directed to polynucleotide sequences excluding one, two, three, four or more of the specific polynucleotide sequences referenced by Genbank Accession No. for each Contig Id which may be included in column five of Table 7. In no way is this listing meant to encompass all of the sequences which may be excluded by the general formula, it is just a representative example. All references available through these accessions are hereby incorporated by reference in their entirety.

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Abstract

Cette invention concerne des polynucléotides nouvellement identifiés liés au colon et au cancer du colon ainsi que les polypeptides codés par ces polynucléotides connus ici collectivement sous l'appellation d'"antigènes du cancer du colon", ainsi que l'utilisation de ces antigènes du cancer du colon pour cibler des types de cellules spécifiques et/ou diagnostiquer, détecter, prévenir et traiter des troubles du colon, notamment la présence d'un cancer du colon et de métastases de cancer du colon. Cette invention concerne des antigènes du cancer du colon de même que des vecteurs, des cellules hôtes, des anticorps dirigés contre les antigènes du cancer du colon ainsi que des méthodes de recombinaison ou de synthèse permettant leur production. L'invention concerne également des méthodes diagnostiques permettant de diagnostiquer et de traiter, de prévenir et/ou pronostiquer des troubles relatifs au colon, notamment le cancer du colon, et des méthodes thérapeutiques de traitement de ces troubles. De plus, l'invention concerne des méthodes de criblage permettant d'identifier des agonistes ainsi que des antagonistes d'antigènes du cancer du colon de l'invention. En outre, l'invention concerne l'inhibition de la production et de la fonction des polypeptides de la présente invention.
EP00966944A 1999-09-29 2000-09-28 Polynucleotides et polypeptides associes au colon et au cancer du colon Withdrawn EP1265582A2 (fr)

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US157137P 1999-09-29
US16328099P 1999-11-03 1999-11-03
US163280P 1999-11-03
PCT/US2000/026524 WO2001022920A2 (fr) 1999-09-29 2000-09-28 Polynucleotides et polypeptides associes au colon et au cancer du colon

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CA2384713A1 (fr) 2001-04-05
US20030109690A1 (en) 2003-06-12

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